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- Software:PeptideProphet (1728 bytes)
5: ... orginally develped at the SPC, part of the ISB. PeptideProphet is now a core part of the Trans-Proteomic Pipelin...
Page text matches
- TPP:V5Feedback (11460 bytes)
84: ...the protein link in the pepxmlviewer when viewing peptideprophet results of spectrast results causes an cgi crash ...
92: ...lot error as before, on pepxmlviewer when viewing peptideprophet results of spectrast results</s>. Displayed when... - TPP:Developer Documentation (23931 bytes)
228: #Run PeptideProphet
229: PeptideProphetParser interact.xml
297: ====PeptideProphetParser====
298: PeptideProphetParser interact.xml (EXCLUDE) (LEAVE) (ICAT) (NOIC...
299: Runs PeptideProphet with options and ''overwrites results to interact... - Software:Overview (3074 bytes)
9: ...ia|Petunia (TPP GUI)]], [[Software:PeptideProphet|PeptideProphet]], [[Software:ProteinProphet|ProteinProphet]], [[... - TPP:Frequently Asked Questions (5647 bytes)
43: *Use CLEVEL when the data is misbehaving and PeptideProphet model is under-predicting the error when compared... - TPP:7.0.0 Release Notes (6884 bytes)
34: === [PeptideProphet:] === - Software:PeptideProphet (1728 bytes)
5: ... orginally develped at the SPC, part of the ISB. PeptideProphet is now a core part of the Trans-Proteomic Pipelin... - Software:ProteinProphet (6941 bytes)
5: ... data. ProteinProphet makes use of results from PeptideProphet, which produces validation results for peptide se...
17: MINPROB: pepeptideProphet probabilty threshold (default=0.05)
40: ...sing by ProteinProphet. It can be used to combine PeptideProphet results from several experiments and search engin...
48: ...least 3 peptides, each observed more than once at PeptideProphet P>0.9, etc), and then count decoys to estimate FD... - Software:Pep3D (1087 bytes)
8: ...e via an INTERACT or pepXML Viewer interface with PeptideProphet results, sequencing attempts and identification q...
17: [[image:pep3d.jpg]] - Software:TPP (8915 bytes)
5: [[image:TPP.jpg|1200px]]
7: image:TPP.jpg|
15: ....proteomecenter.org/wiki/index.php?title=Software:PeptideProphet]]
59: [[Software:PeptideProphet|PeptideProphet]]: Statistical validation of PSMs using search en...
61: ...uence validation, using [[Software:PeptideProphet|PeptideProphet]] results; can also combine the results of multip... - TPP 7.0.0: Installing on Ubuntu 22.04 LTS (11616 bytes)
2: |[[Image:alert.jpg|middle|left]]
175: ...installation with a very quick Comet search and a PeptideProphet->iProphet->ProteinProphet->mzIdentML processing, ...
226: - Under -PEPTIDEPROPHET OPTIONS- check box next to "Use accurate mass bin... - TPP:X!Tandem and the TPP (5454 bytes)
19: ...nd the TPP. Currently, we continue to refine the PeptideProphet models for X!Tandem-Kscore.
26: ...m features (e.g. some refinement options) because PeptideProphet may not work with them. - TPP:Phenyx and the TPP (323 bytes)
5: ...ions for working on the command-line, issues with PeptideProphet modeling (if any.) - Software:SpectraST (70083 bytes)
155: ...s assigned. (iProphet probabilities are used over PeptideProphet ones if both are present.)
242: ...coy counting method, and improves the accuracy of PeptideProphet in validating spectral search results.
604: ...as the weight.<br>-c_WGTP = Use a function of the PeptideProphet probability as the weight.
723: ...ually look for the .none file, but the resulting .jpg file will be named with the same prefix as the .n... - TPP Tutorial v1 (43187 bytes)
19: [[image:Pipeline_Tutorial.jpg]]
212: [[Image:sequest_params.jpg]]
247: ===PeptideProphet===
256: ...et’ and ‘Use ICAT information’ under the ‘PeptideProphet Options’.'''
258: ...ly validate database search results. In addition, PeptideProphet results can facilitate the benchmarking of variou... - Export questions discussion list (2232 bytes)
37: 4) Should we use a consistent PeptideProphet cutoff for our lists? Peptide Atlas builds use 0... - Expert search and TPP usage (12929 bytes)
67: * -O (letter, not digit) introduces options for PeptideProphet
77: * See if the PeptideProphet modeling failed for any of the charge states. If ...
86: PeptideProphet <spectra-searched><spectra-identified> <fraction>...
88: ...gnitude different from the PepPro FDR. Otherwise, PeptideProphet is not modeling the data well and you should cons... - Terry's blog (18394 bytes)
38: ...ods. Can use QualScore (advantage: learn Java) or PeptideProphet as base code?
44: * Don't use PeptideProphet to merge results from different samples (as I've ...
46: * '''NTT''' option in PeptideProphet makes a huge difference in the probabilities.
76: * Establish this practice: always run xinteract (PeptideProphet) with -E (experiment_label) flag. This will make ...
78: ...ent. So we don't want to pre-filter peptides with PeptideProphet probs < 0.9. Instead, we hard-coded createPipelin... - Building Peptide Atlas (26978 bytes)
13: ===Start with one or more PeptideProphet output files (pepXML) for each experiment in each...
14: ... runtandemsearch automatically run iProphet after PeptideProphet.
16: ...rently, for SpectraST, RefreshParser is run after PeptideProphet by finishspectrastsearch. If this is not necessar...
39: ...nd did not run iProphet immediately after running PeptideProphet, run it now. - TPP Tandem search (19915 bytes)
276: [[Software:PeptideProphet | PeptideProphet]] uses a statistical approach to filter incorrect...
293: ... level analysis using [[Software:PeptideProphet | PeptideProphet]] and [[Software:ProteinProphet | ProteinProphet]... - Software:Mayu (3991 bytes)
78: the discriminant score (e.g. PeptideProphet, xcorr, mascot ion
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